Trouble uploading .hic to browser
Seth Weaver
Hello,
I am having trouble loading on a .hic track that I made with Juicer Tools Pre to the browser. The data that I am using is for all of chr17 in the hg38 assembly and is currently in the ‘short with score format’ The exact command I ran to create the .hic file from a ‘short with score format’ contact matrix is:
java -Xmx30g -jar juicer_tools_2.17.00.jar pre -c chr17 -r 10000 hicShortWithScoreChr17NoZero.txt fullHg38Chr17output.hic hg38
This command seems to run without errors. I placed this file on an https server and then tried to load it as a custom track to browser with:
track type=hic name="My HIC" bigDataUrl=https://vertgenlab.cloud.duke.edu/seth/fullHg38Chr17output.hic
When I do this the error message that I get from the browser is: ‘getline failure when reading file’ and no data shows up on the browser. As a test, I downloaded a .hic file from another source and uploaded it in the same manner, this .hic file uploaded correctly. The headers of my file vs the one I downloaded appear to be a bit different, if that matters. I am wondering if you would happen to know what was going on, either in the making of the .hic file using Juicer Tools Pre or in the uploading of my .hic file that is returning this error. Any help would be much appreciated! I am happy to send any of the files that I have referenced if you would like to take a look at them.
Thanks!
Seth
Gerardo Perez
Hello, Seth.
Thank you for your interest in the Genome Browser and your question about uploading a hic file to the browser.
Which juicer version did you use to create the hic file? We have seen a similar issue due to incompatibilities between the juicer library versions. Our tools that read the hic files were built when hic files were on version 7, and new juicer versions cause issues.
We are looking into updating our software, but we have limited bandwidth and cannot offer a timeline for when that will happen.
If the juicer version is newer than version 7, you could create the same hic file with an older version of juicer, and it should work.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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Seth Weaver
Gerardo,
Yes, I was using a newer version of Juicer! This is exactly the information I needed.
Thanks for the help!
Seth
Danilo Dubocanin
Gerardo Perez
Thank you for your interest in the Genome Browser.
Could you share the URL to your HIC file with the same problem? You can send it to our confidential support list at genom...@soe.ucsc.edu. We can check for the various components, such as the file version, byte-range access, etc. We think the problem might be a version issue, and unfortunately, adding support for the latest juicer HIC version is still in our work queue. We do not have a timeline for when we will update our software to support the latest HIC files.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team.
UCSC Genomics Institute